1
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Andersson E, Rothenberg EV, Peterson C, Olariu V. T-cell commitment inheritance-an agent-based multi-scale model. NPJ Syst Biol Appl 2024; 10:40. [PMID: 38632273 PMCID: PMC11024127 DOI: 10.1038/s41540-024-00368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations predicted that the commitment is a three-step process that occurs on average over several cell generations once a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function approximately two to three generations later. This is when our LCA analysis indicates that the decision to commit is taken even though in general another one to two generations elapse before the cell actually becomes committed by transitioning to the DN2b state. Our results showed that there is decision inheritance in the commitment mechanism.
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Affiliation(s)
- Emil Andersson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Carsten Peterson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Victor Olariu
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden.
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2
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Spolski R, Li P, Chandra V, Shin B, Goel S, Sakamoto K, Liu C, Oh J, Ren M, Enomoto Y, West EE, Christensen SM, Wan ECK, Ge M, Lin JX, Yan B, Kazemian M, Yu ZX, Nagao K, Vijayanand P, Rothenberg EV, Leonard WJ. Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function. Sci Immunol 2023; 8:eadi8217. [PMID: 37922339 PMCID: PMC10832512 DOI: 10.1126/sciimmunol.adi8217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/10/2023] [Indexed: 11/05/2023]
Abstract
The IL-2 receptor α chain (IL-2Rα/CD25) is constitutively expressed on double-negative (DN2/DN3 thymocytes and regulatory T cells (Tregs) but induced by IL-2 on T and natural killer (NK) cells, with Il2ra expression regulated by a STAT5-dependent super-enhancer. We investigated CD25 regulation and function using a series of mice with deletions spanning STAT5-binding elements. Deleting the upstream super-enhancer region mainly affected constitutive CD25 expression on DN2/DN3 thymocytes and Tregs, with these mice developing autoimmune alopecia, whereas deleting an intronic region decreased IL-2-induced CD25 on peripheral T and NK cells. Thus, distinct super-enhancer elements preferentially control constitutive versus inducible expression in a cell type-specific manner. The mediator-1 coactivator colocalized with specific STAT5-binding sites. Moreover, both upstream and intronic regions had extensive chromatin interactions, and deletion of either region altered the super-enhancer structure in mature T cells. These results demonstrate differential functions for distinct super-enhancer elements, thereby indicating previously unknown ways to manipulate CD25 expression in a cell type-specific fashion.
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Affiliation(s)
- Rosanne Spolski
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peng Li
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vivek Chandra
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shubham Goel
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keiko Sakamoto
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Hamamatsu University School of Medicine, Department of Dermatology, Hamamatsu, Japan
| | - Chengyu Liu
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jangsuk Oh
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Min Ren
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yutaka Enomoto
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erin E West
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M Christensen
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edwin C K Wan
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meili Ge
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Zu-Xi Yu
- Pathology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keisuke Nagao
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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3
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Andersson E, Rothenberg EV, Peterson C, Olariu V. T-cell commitment inheritance - an agent-based multi-scale model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562905. [PMID: 37905091 PMCID: PMC10614897 DOI: 10.1101/2023.10.18.562905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations showed that the commitment is a three-step process over several cell generations where a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function two to three generations later which is when the decision to commit is taken. Finally, after another one to two generations, the cell becomes committed by transitioning to the DN2b state. Our results showed that there is inheritance in the commitment mechanism.
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Affiliation(s)
- Emil Andersson
- Computational Biology and Biological Physics, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carsten Peterson
- Computational Biology and Biological Physics, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Victor Olariu
- Computational Biology and Biological Physics, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
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4
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Xu Z, He L, Wu Y, Yang L, Li C, Wu H. PTEN regulates hematopoietic lineage plasticity via PU.1-dependent chromatin accessibility. Cell Rep 2023; 42:112967. [PMID: 37561626 DOI: 10.1016/j.celrep.2023.112967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
PTEN loss in fetal liver hematopoietic stem cells (HSCs) leads to alterations in myeloid, T-, and B-lineage potentials and T-lineage acute lymphoblastic leukemia (T-ALL) development. To explore the mechanism underlying PTEN-regulated hematopoietic lineage choices, we carry out integrated assay for transposase-accessible chromatin using sequencing (ATAC-seq), single-cell RNA-seq, and in vitro culture analyses using in vivo-isolated mouse pre-leukemic HSCs and progenitors. We find that PTEN loss alters chromatin accessibility of key lineage transcription factor (TF) binding sites at the prepro-B stage, corresponding to increased myeloid and T-lineage potentials and reduced B-lineage potential. Importantly, we find that PU.1 is an essential TF downstream of PTEN and that altering PU.1 levels can reprogram the chromatin accessibility landscape and myeloid, T-, and B-lineage potentials in Ptennull prepro-B cells. Our study discovers prepro-B as the key developmental stage underlying PTEN-regulated hematopoietic lineage choices and suggests a critical role of PU.1 in modulating the epigenetic state and lineage plasticity of prepro-B progenitors.
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Affiliation(s)
- Zihan Xu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Center for Statistical Science, Peking University, Beijing, China
| | - Libing He
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Cheng Li
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Center for Statistical Science, Peking University, Beijing, China.
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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5
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Kuintzle R, Santat LA, Elowitz MB. Diversity in Notch ligand-receptor signaling interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554677. [PMID: 37662208 PMCID: PMC10473737 DOI: 10.1101/2023.08.24.554677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The Notch signaling pathway uses families of ligands and receptors to transmit signals to nearby cells. These components are expressed in diverse combinations in different cell types, interact in a many-to-many fashion, both within the same cell (in cis) and between cells (in trans), and their interactions are modulated by Fringe glycosyltransferases. A fundamental question is how the strength of Notch signaling depends on which pathway components are expressed, at what levels, and in which cells. Here, we used a quantitative, bottom-up, cell-based approach to systematically characterize trans-activation, cis-inhibition, and cis-activation signaling efficiencies across a range of ligand and Fringe expression levels in two mammalian cell types. Each ligand (Dll1, Dll4, Jag1, and Jag2) and receptor variant (Notch1 and Notch2) analyzed here exhibited a unique profile of interactions, Fringe-dependence, and signaling outcomes. All four ligands were able to bind receptors in cis and in trans, and all ligands trans-activated both receptors except for Jag1, which failed to activate Notch1. Cis-interactions were predominantly inhibitory, with the exception of the Dll1- and Dll4-Notch2 pairs, which exhibited cis-activation stronger than trans-activation. Lfng strengthened Delta-mediated trans-activation and weakened Jagged-mediated trans-activation for both receptors. Finally, cis-ligands showed diverse cis-inhibition strengths, which depended on the identity of the trans-ligand as well as the receptor. The map of receptor-ligand-Fringe interaction outcomes revealed here should help guide rational perturbation and control of the Notch pathway.
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Affiliation(s)
- Rachael Kuintzle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Leah A. Santat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
| | - Michael B. Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
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6
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MacNabb BW, Rothenberg EV. Speed and navigation control of thymocyte development by the fetal T-cell gene regulatory network. Immunol Rev 2023; 315:171-196. [PMID: 36722494 PMCID: PMC10771342 DOI: 10.1111/imr.13190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
T-cell differentiation is a tightly regulated developmental program governed by interactions between transcription factors (TFs) and chromatin landscapes and affected by signals received from the thymic stroma. This process is marked by a series of checkpoints: T-lineage commitment, T-cell receptor (TCR)β selection, and positive and negative selection. Dynamically changing combinations of TFs drive differentiation along the T-lineage trajectory, through mechanisms that have been most extensively dissected in adult mouse T-lineage cells. However, fetal T-cell development differs from adult in ways that suggest that these TF mechanisms are not fully deterministic. The first wave of fetal T-cell differentiation occurs during a unique developmental window during thymic morphogenesis, shows more rapid kinetics of differentiation with fewer rounds of cell division, and gives rise to unique populations of innate lymphoid cells (ILCs) and invariant γδT cells that are not generated in the adult thymus. As the characteristic kinetics and progeny biases are cell-intrinsic properties of thymic progenitors, the differences could be based on distinct TF network circuitry within the progenitors themselves. Here, we review recent single-cell transcriptome data that illuminate the TF networks involved in T-cell differentiation in the fetal and adult mouse thymus.
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Affiliation(s)
- Brendan W MacNabb
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California, USA
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7
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Bhansali RS, Barta SK. Central Nervous System Progression/Relapse in Mature T- and NK-Cell Lymphomas. Cancers (Basel) 2023; 15:925. [PMID: 36765882 PMCID: PMC9913807 DOI: 10.3390/cancers15030925] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Non-Hodgkin lymphomas (NHL) are cancers of mature B-, T-, and NK-cells which display marked biological heterogeneity between different subtypes. Mature T- and NK-cell neoplasms are an often-aggressive subgroup of NHL and make up approximately 15% of all NHL. Long-term follow up studies have demonstrated that patients with relapsed/refractory disease have dismal outcomes; in particular, secondary central nervous system (CNS) involvement is associated with higher mortality, though it remains controversial whether this independently confers worse outcomes or if it simply reflects more aggressive systemic disease. Possible risk factors predictive of CNS involvement, such as an elevated lactate dehydrogenase and more than two sites of extranodal involvement, may suggest the latter, though several studies have suggested that discrete sites of anatomic involvement or tumor histology may be independent risk factors as well. Ultimately, small retrospective case series form the basis of our understanding of this rare but devastating event but have not yet demonstrated a consistent benefit of CNS-directed prophylaxis in preventing this outcome. Nonetheless, ongoing efforts are working to establish the epidemiology of CNS progression/relapse in mature T- and NK-cell lymphomas with the goal of identifying clinicopathologic risk factors, which may potentially help discern which patients may benefit from CNS-directed prophylactic therapy or more aggressive systemic therapy.
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Affiliation(s)
| | - Stefan K. Barta
- Department of Medicine, Division of Hematology and Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
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8
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Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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9
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Wang X, Liu S, Yu J. Multi-lineage Differentiation from Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:159-175. [PMID: 38228964 DOI: 10.1007/978-981-99-7471-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The hematopoietic stem cells (HSCs) have the ability to differentiate and give rise to all mature blood cells. Commitment to differentiation progressively limits the self-renewal potential of the original HSCs by regulating the level of lineage-specific gene expression. In this review, we will summarize the current understanding of the molecular mechanisms underlying HSC differentiation toward erythroid, myeloid, and lymphocyte lineages. Moreover, we will decipher how the single-cell technologies advance the lineage-biased HSC subpopulations and their differentiation potential.
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Affiliation(s)
- Xiaoshuang Wang
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
| | - Siqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
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10
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Rodríguez-Caparrós A, Tani-ichi S, Casal Á, López-Ros J, Suñé C, Ikuta K, Hernández-Munain C. Interleukin-7 receptor signaling is crucial for enhancer-dependent TCRδ germline transcription mediated through STAT5 recruitment. Front Immunol 2022; 13:943510. [PMID: 36059467 PMCID: PMC9437428 DOI: 10.3389/fimmu.2022.943510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
γδ T cells play important roles in immune responses by rapidly producing large quantities of cytokines. Recently, γδ T cells have been found to be involved in tissue homeostatic regulation, playing roles in thermogenesis, bone regeneration and synaptic plasticity. Nonetheless, the mechanisms involved in γδ T-cell development, especially the regulation of TCRδ gene transcription, have not yet been clarified. Previous studies have established that NOTCH1 signaling plays an important role in the Tcrg and Tcrd germline transcriptional regulation induced by enhancer activation, which is mediated through the recruitment of RUNX1 and MYB. In addition, interleukin-7 signaling has been shown to be required for Tcrg germline transcription, VγJγ rearrangement and γδ T-lymphocyte generation as well as for promoting T-cell survival. In this study, we discovered that interleukin-7 is required for the activation of enhancer-dependent Tcrd germline transcription during thymocyte development. These results indicate that the activation of both Tcrg and Tcrd enhancers during γδ T-cell development in the thymus depends on the same NOTCH1- and interleukin-7-mediated signaling pathways. Understanding the regulation of the Tcrd enhancer during thymocyte development might lead to a better understanding of the enhancer-dependent mechanisms involved in the genomic instability and chromosomal translocations that cause leukemia.
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Affiliation(s)
- Alonso Rodríguez-Caparrós
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Shizue Tani-ichi
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Áurea Casal
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Jennifer López-Ros
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Carlos Suñé
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
- *Correspondence: Cristina Hernández-Munain,
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11
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Zhou W, Gao F, Romero-Wolf M, Jo S, Rothenberg EV. Single-cell deletion analyses show control of pro-T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b. Sci Immunol 2022; 7:eabm1920. [PMID: 35594339 PMCID: PMC9273332 DOI: 10.1126/sciimmunol.abm1920] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
As early T cell precursors transition from multipotentiality to T lineage commitment, they change expression of multiple transcription factors. It is unclear whether individual transcription factors directly control choices between T cell identity and some alternative fate or whether these factors mostly affect proliferation or survival during the normal commitment process. Here, we unraveled the impacts of deleting individual transcription factors at two stages in early T cell development, using synchronized in vitro differentiation systems, single-cell RNA-seq with batch indexing, and controlled gene-disruption strategies. First, using a customized method for single-cell CRISPR disruption, we defined how the early-acting transcription factors Bcl11a, Erg, Spi1 (PU.1), Gata3, and Tcf7 (TCF1) function before commitment. The results revealed a kinetic tug of war within individual cells between T cell factors Tcf7 and Gata3 and progenitor factors Spi1 and Bcl11a, with an unexpected guidance role for Erg. Second, we tested how activation of transcription factor Bcl11b during commitment altered ongoing cellular programs. In knockout cells where Bcl11b expression was prevented, the cells did not undergo developmental arrest, instead following an alternative path as T lineage commitment was blocked. A stepwise, time-dependent regulatory cascade began with immediate-early transcription factor activation and E protein inhibition, finally leading Bcl11b knockout cells toward exit from the T cell pathway. Last, gene regulatory networks of transcription factor cross-regulation were extracted from the single-cell transcriptome results, characterizing the specification network operating before T lineage commitment and revealing its links to both the Bcl11b knockout alternative network and the network consolidating T cell identity during commitment.
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Affiliation(s)
- Wen Zhou
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
- Program in Biochemistry and Molecular Biophysics, California Institute of Technology
- Current address: BillionToOne, Menlo Park, CA
| | - Fan Gao
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
- Caltech Bioinformatics Resource Center, Beckman Institute of Caltech
| | - Maile Romero-Wolf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
- Current address: Center for Stem Cell Biology and Regenerative Medicine, University of Southern California
| | - Suin Jo
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
- Current address: Washington University of St. Louis
| | - Ellen V. Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
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12
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Fishman H, Madiwale S, Geron I, Bari V, Van Loocke W, Kirschenbaum Y, Ganmore I, Kugler E, Rein-Gil A, Friedlander G, Schiby G, Birger Y, Strehl S, Soulier J, Knoechel B, Ferrando A, Noy-Lotan S, Nagler A, Mulloy JC, Van Vlierberghe P, Izraeli S. ETV6-NCOA2 fusion induces T/myeloid mixed-phenotype leukemia through transformation of nonthymic hematopoietic progenitor cells. Blood 2022; 139:399-412. [PMID: 34624096 PMCID: PMC9906988 DOI: 10.1182/blood.2020010405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 09/26/2021] [Indexed: 01/05/2023] Open
Abstract
Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. The pathogenesis is largely unknown, and the treatment is challenging. We previously reported the specific association of the recurrent t(8;12)(q13;p13) chromosomal translocation that creates the ETV6-NCOA2 fusion with T/myeloid leukemias. Here we report that ETV6-NCOA2 initiates T/myeloid leukemia in preclinical models; ectopic expression of ETV6-NCOA2 in mouse bone marrow hematopoietic progenitors induced T/myeloid lymphoma accompanied by spontaneous Notch1-activating mutations. Similarly, cotransduction of human cord blood CD34+ progenitors with ETV6-NCOA2 and a nontransforming NOTCH1 mutant induced T/myeloid leukemia in immunodeficient mice; the immunophenotype and gene expression pattern were similar to those of patient-derived ETV6-NCOA2 leukemias. Mechanistically, we show that ETV6-NCOA2 forms a transcriptional complex with ETV6 and the histone acetyltransferase p300, leading to derepression of ETV6 target genes. The expression of ETV6-NCOA2 in human and mouse nonthymic hematopoietic progenitor cells induces transcriptional dysregulation, which activates a lymphoid program while failing to repress the expression of myeloid genes such as CSF1 and MEF2C. The ETV6-NCOA2 induced arrest at an early immature T-cell developmental stage. The additional acquisition of activating NOTCH1 mutations transforms the early immature ETV6-NCOA2 cells into T/myeloid leukemias. Here, we describe the first preclinical model to depict the initiation of T/myeloid leukemia by a specific somatic genetic aberration.
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Affiliation(s)
- Hila Fishman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Shreyas Madiwale
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Ifat Geron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Vase Bari
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | - Wouter Van Loocke
- Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - Yael Kirschenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Itamar Ganmore
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Eitan Kugler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Avigail Rein-Gil
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ginette Schiby
- Institute for Pathology Laboratory, Hematology Institute, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Yehudit Birger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Sabine Strehl
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Jean Soulier
- Genomes and Cell Biology of Disease, Hôpital Saint-Louis, Paris, France
| | - Birgit Knoechel
- Dana-Farber Cancer Institute, Boston Children's Hospital, Boston, MA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Sharon Noy-Lotan
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Arnon Nagler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Hematology Division Bone Marrow Transplants and Cord-Blood Bank, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - James C. Mulloy
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | | | - Shai Izraeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
- Department of System Biology, City of Hope, Duarte, CA
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13
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OUP accepted manuscript. Brief Funct Genomics 2022; 21:159-176. [DOI: 10.1093/bfgp/elac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
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14
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Van Thillo Q, De Bie J, Seneviratne JA, Demeyer S, Omari S, Balachandran A, Zhai V, Tam WL, Sweron B, Geerdens E, Gielen O, Provost S, Segers H, Boeckx N, Marshall GM, Cheung BB, Isobe K, Kato I, Takita J, Amos TG, Deveson IW, McCalmont H, Lock RB, Oxley EP, Garwood MM, Dickins RA, Uyttebroeck A, Carter DR, Cools J, de Bock CE. Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia. Nat Commun 2021; 12:4164. [PMID: 34230493 PMCID: PMC8260768 DOI: 10.1038/s41467-021-24442-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Spi-1 Proto-Oncogene (SPI1) fusion genes are recurrently found in T-cell acute lymphoblastic leukemia (T-ALL) cases but are insufficient to drive leukemogenesis. Here we show that SPI1 fusions in combination with activating NRAS mutations drive an immature T-ALL in vivo using a conditional bone marrow transplant mouse model. Addition of the oncogenic fusion to the NRAS mutation also results in a higher leukemic stem cell frequency. Mechanistically, genetic deletion of the β-catenin binding domain within Transcription factor 7 (TCF7)-SPI1 or use of a TCF/β-catenin interaction antagonist abolishes the oncogenic activity of the fusion. Targeting the TCF7-SPI1 fusion in vivo with a doxycycline-inducible knockdown results in increased differentiation. Moreover, both pharmacological and genetic inhibition lead to down-regulation of SPI1 targets. Together, our results reveal an example where TCF7-SPI1 leukemia is vulnerable to pharmacological targeting of the TCF/β-catenin interaction.
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Affiliation(s)
- Quentin Van Thillo
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Jolien De Bie
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, UZ Leuven, Leuven, Belgium
| | - Janith A Seneviratne
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sofie Demeyer
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofia Omari
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Anushree Balachandran
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Vicki Zhai
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Wai L Tam
- Technology Innovation Lab, VIB, Gent, Belgium
| | - Bram Sweron
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ellen Geerdens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sarah Provost
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
| | - Glenn M Marshall
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Belamy B Cheung
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kiyotaka Isobe
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Timothy G Amos
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Hannah McCalmont
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ethan P Oxley
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Maximilian M Garwood
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Anne Uyttebroeck
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Daniel R Carter
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia
| | - Jan Cools
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
| | - Charles E de Bock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia.
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15
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Chiara VD, Daxinger L, Staal FJT. The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors. Cells 2021; 10:1074. [PMID: 33946533 PMCID: PMC8147249 DOI: 10.3390/cells10051074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
Hematopoietic multipotent progenitors seed the thymus and then follow consecutive developmental stages until the formation of mature T cells. During this process, phenotypic changes of T cells entail stage-specific transcriptional programs that underlie the dynamic progression towards mature lymphocytes. Lineage-specific transcription factors are key drivers of T cell specification and act in conjunction with epigenetic regulators that have also been elucidated as crucial players in the establishment of regulatory networks necessary for proper T cell development. In this review, we summarize the activity of transcription factors and epigenetic regulators that together orchestrate the intricacies of early T cell development with a focus on regulation of T cell lineage commitment.
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Affiliation(s)
- Veronica Della Chiara
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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16
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Rothenberg EV. Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment. Biophys J 2021; 120:4162-4181. [PMID: 33838137 PMCID: PMC8516641 DOI: 10.1016/j.bpj.2021.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Transcription factors are the major agents that read the regulatory sequence information in the genome to initiate changes in expression of specific genes, both in development and in physiological activation responses. Their actions depend on site-specific DNA binding and are largely guided by their individual DNA target sequence specificities. However, their action is far more conditional in a real developmental context than would be expected for simple reading of local genomic DNA sequence, which is common to all cells in the organism. They are constrained by slow-changing chromatin states and by interactions with other transcription factors, which affect their occupancy patterns of potential sites across the genome. These mechanisms lead to emergent discontinuities in function even for transcription factors with minimally changing expression. This is well revealed by diverse lineages of blood cells developing throughout life from hematopoietic stem cells, which use overlapping combinations of transcription factors to drive strongly divergent gene regulation programs. Here, using development of T lymphocytes from hematopoietic multipotent progenitor cells as a focus, recent evidence is reviewed on how binding specificity and dynamics, transcription factor cooperativity, and chromatin state changes impact the effective regulatory functions of key transcription factors including PU.1, Runx1, Notch-RBPJ, and Bcl11b.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.
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17
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Romero-Wolf M, Shin B, Zhou W, Koizumi M, Rothenberg EV, Hosokawa H. Notch2 complements Notch1 to mediate inductive signaling that initiates early T cell development. J Cell Biol 2021; 219:152003. [PMID: 32756905 PMCID: PMC7659720 DOI: 10.1083/jcb.202005093] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Notch signaling is the dominant intercellular signaling input during the earliest stages of T cell development in the thymus. Although Notch1 is known to be indispensable, we show that it does not mediate all Notch signaling in precommitment stages: Notch2 initially works in parallel to promote early murine T cell development and antagonize other fates. Notch-regulated target genes before and after T lineage commitment change dynamically, and we show that this partially reflects shifts in genome-wide DNA binding by RBPJ, the transcription factor activated by complex formation with the Notch intracellular domain. Although Notch signaling and transcription factor PU.1 can activate some common targets in precommitment T progenitors, Notch signaling and PU.1 activity have functionally antagonistic effects on multiple targets, delineating separation of pro-T cells from alternative PU.1-dependent fates. These results define a distinct mechanism of Notch signal response that distinguishes the initial stages of murine T cell development.
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Affiliation(s)
- Maile Romero-Wolf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Boyoung Shin
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Wen Zhou
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Hiroyuki Hosokawa
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA.,Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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18
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Rothenberg EV. Single-cell insights into the hematopoietic generation of T-lymphocyte precursors in mouse and human. Exp Hematol 2021; 95:1-12. [PMID: 33454362 PMCID: PMC8018899 DOI: 10.1016/j.exphem.2020.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 01/29/2023]
Abstract
T-Cell development is a major branch of lymphoid development and a key output of hematopoiesis, especially in early life, but the molecular requirements for T-cell potential have remained obscure. Considerable advances have now been made toward solving this problem through single-cell transcriptome studies, interfaced with in vitro differentiation assays that monitor potential efficiently at the single-cell level. This review focuses on a series of recent reports studying mouse and human early T-cell precursors, both in the developing fetus and in stringently purified postnatal samples of intrathymic and prethymic T-lineage precursors. Cross-comparison of results reveals a robustly conserved core program in mouse and human, but with some informative and provocative variations between species and between ontogenic states. Repeated findings are the multipotent progenitor regulatory signature of thymus-seeding cells and the proximity of the T-cell program to dendritic cell programs, especially to plasmacytoid dendritic cells in humans.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA.
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19
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Hosokawa H, Rothenberg EV. How transcription factors drive choice of the T cell fate. Nat Rev Immunol 2021; 21:162-176. [PMID: 32918063 PMCID: PMC7933071 DOI: 10.1038/s41577-020-00426-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Recent evidence has elucidated how multipotent blood progenitors transform their identities in the thymus and undergo commitment to become T cells. Together with environmental signals, a core group of transcription factors have essential roles in this process by directly activating and repressing specific genes. Many of these transcription factors also function in later T cell development, but control different genes. Here, we review how these transcription factors work to change the activities of specific genomic loci during early intrathymic development to establish T cell lineage identity. We introduce the key regulators and highlight newly emergent insights into the rules that govern their actions. Whole-genome deep sequencing-based analysis has revealed unexpectedly rich relationships between inherited epigenetic states, transcription factor-DNA binding affinity thresholds and influences of given transcription factors on the activities of other factors in the same cells. Together, these mechanisms determine T cell identity and make the lineage choice irreversible.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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20
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Hosokawa H, Masuhara K, Koizumi M. Transcription factors regulate early T cell development via redeployment of other factors: Functional dynamics of constitutively required factors in cell fate decisions. Bioessays 2021; 43:e2000345. [PMID: 33624856 DOI: 10.1002/bies.202000345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 01/02/2023]
Abstract
Establishment of cell lineage identity from multipotent progenitors is controlled by cooperative actions of lineage-specific and stably expressed transcription factors, combined with input from environmental signals. Lineage-specific master transcription factors activate and repress gene expression by recruiting consistently expressed transcription factors and chromatin modifiers to their target loci. Recent technical advances in genome-wide and multi-omics analysis have shed light on unexpected mechanisms that underlie more complicated actions of transcription factors in cell fate decisions. In this review, we discuss functional dynamics of stably expressed and continuously required factors, Notch and Runx family members, throughout developmental stages of early T cell development in the thymus. Pre- and post-commitment stage-specific transcription factors induce dynamic redeployment of Notch and Runx binding genomic regions. Thus, together with stage-specific transcription factors, shared transcription factors across distinct developmental stages regulate acquisition of T lineage identity.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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21
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Olariu V, Yui MA, Krupinski P, Zhou W, Deichmann J, Andersson E, Rothenberg EV, Peterson C. Multi-scale Dynamical Modeling of T Cell Development from an Early Thymic Progenitor State to Lineage Commitment. Cell Rep 2021; 34:108622. [PMID: 33440162 DOI: 10.1016/j.celrep.2020.108622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/24/2020] [Accepted: 12/18/2020] [Indexed: 01/13/2023] Open
Abstract
Intrathymic development of committed progenitor (pro)-T cells from multipotent hematopoietic precursors offers an opportunity to dissect the molecular circuitry establishing cell identity in response to environmental signals. This transition encompasses programmed shutoff of stem/progenitor genes, upregulation of T cell specification genes, proliferation, and ultimately commitment. To explain these features in light of reported cis-acting chromatin effects and experimental kinetic data, we develop a three-level dynamic model of commitment based upon regulation of the commitment-linked gene Bcl11b. The levels are (1) a core gene regulatory network (GRN) architecture from transcription factor (TF) perturbation data, (2) a stochastically controlled chromatin-state gate, and (3) a single-cell proliferation model validated by experimental clonal growth and commitment kinetic assays. Using RNA fluorescence in situ hybridization (FISH) measurements of genes encoding key TFs and measured bulk population dynamics, this single-cell model predicts state-switching kinetics validated by measured clonal proliferation and commitment times. The resulting multi-scale model provides a mechanistic framework for dissecting commitment dynamics.
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Affiliation(s)
- Victor Olariu
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Mary A Yui
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pawel Krupinski
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Wen Zhou
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Julia Deichmann
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Emil Andersson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Carsten Peterson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
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22
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Liu Q, Kim MH, Friesen L, Kim CH. BATF regulates innate lymphoid cell hematopoiesis and homeostasis. Sci Immunol 2020; 5:eaaz8154. [PMID: 33277375 PMCID: PMC8375455 DOI: 10.1126/sciimmunol.aaz8154] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 06/01/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022]
Abstract
Early hematopoietic progenitors undergo sophisticated developmental processes to become committed innate lymphoid cell (ILC) progenitors and ultimately mature ILC subsets in the periphery. Basic leucine zipper ATF-like transcription factor (Batf) plays important roles in lymphocyte biology. We report here that Batf regulates the production of bone marrow ILC progenitors and maintenance of peripheral ILCs. The expression of Batf is induced during ILC development at the α-lymphoid progenitor stage in response to the cytokine IL-7. As a potential mechanism, up-regulated Batf binds and activates transcription of the Nfil3 gene to promote ILC hematopoiesis. Batf is necessary to maintain normal numbers of early and late ILC progenitors in the bone marrow and mature ILC1, ILC2, ILC3, and NK cells in most peripheral tissues. Batf deficiency causes ILC lymphopenia, leading to defective ILC responses to inflammatory cytokines and defective immunity to enteric bacterial infections. Thus, Batf plays critical roles in bone marrow hematopoiesis, peripheral homeostasis, and effector functions of ILCs.
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Affiliation(s)
- Qingyang Liu
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
- Mary H. Weiser Food Allergy Center, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Myung H Kim
- Laboratory of Immunology and Hematopoiesis, Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Leon Friesen
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
- Mary H. Weiser Food Allergy Center, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Chang H Kim
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
- Mary H. Weiser Food Allergy Center, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
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23
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Aboulmouna L, Raja R, Khanum S, Gupta S, Maurya MR, Grama A, Subramaniam S, Ramkrishna D. Cybernetic modeling of biological processes in mammalian systems. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2020.100660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Joshi M, Gangenahalli G. Myelopoiesis specific gene expression profiling in human CD34 + hematopoietic stem cells. Gene Expr Patterns 2020; 37:119128. [PMID: 32707324 DOI: 10.1016/j.gep.2020.119128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/31/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
Differentiation of the HSCs into myeloid lineage is primarily monitored by transcription factor PU.1. GATA1 acts as a negative regulator by antagonizing the function of PU.1 by bindings its β3/β4 domain. In this study, a mutation was induced in PU.1 which blocks its interaction with GATA1. The pure form of this mutant protein i.e Y244D was loaded on poly (lactic-co-glycolic acid) nanoparticles to transfect CD34+ cells, which act as a selective tool to enhance the myelopoiesis, as confirmed by flow cytometry analysis. Further, microarray data analysis was performed to gather information on myelopoiesis specific signaling pathways and genes involved in myelopoiesis like CCL2, S100A8, and S100A9, which were also found to be significantly upregulated in the mutant form. Different molecular functions like antioxidant activity, signal transduction, developmental processes, and biological adhesion were analyzed. This study potentially signifies that PU.1 mutant is highly efficient in myelopoiesis.
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Affiliation(s)
- Madhuri Joshi
- Division of Stem Cell & Gene Therapy Research, Institute of Nuclear Medicine & Allied Sciences, Delhi, 110054, India
| | - Gurudutta Gangenahalli
- Division of Stem Cell & Gene Therapy Research, Institute of Nuclear Medicine & Allied Sciences, Research and Development Organization, Delhi, 110054, India.
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25
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Rao TN, Kumar S, Pulikkottil AJ, Oliveri F, Hendriks RW, Beckel F, Fehling HJ. Novel, Non-Gene-Destructive Knock-In Reporter Mice Refute the Concept of Monoallelic Gata3 Expression. THE JOURNAL OF IMMUNOLOGY 2020; 204:2600-2611. [PMID: 32213568 DOI: 10.4049/jimmunol.2000025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/26/2020] [Indexed: 02/04/2023]
Abstract
Accurately tuned expression levels of the transcription factor GATA-3 are crucial at several stages of T cell and innate lymphoid cell development and differentiation. Moreover, several lines of evidence suggest that Gata3 expression might provide a reliable molecular marker for the identification of elusive progenitor cell subsets at the earliest stages of T lineage commitment. To be able to faithfully monitor Gata3 expression noninvasively at the single-cell level, we have generated a novel strain of knock-in reporter mice, termed GATIR, by inserting an expression cassette encoding a bright fluorescent marker into the 3'-untranslated region of the endogenous Gata3 locus. Importantly, in contrast to three previously published strains of Gata3 reporter mice, GATIR mice preserve physiological Gata3 expression on the targeted allele. In this study, we show that GATIR mice faithfully reflect endogenous Gata3 expression without disturbing the development of GATA-3-dependent lymphoid cell populations. We further show that GATIR mice provide an ideal tool for noninvasive monitoring of Th2 polarization and straightforward identification of innate lymphoid cell 2 progenitor populations. Finally, as our reporter is non-gene-destructive, GATIR mice can be bred to homozygosity, not feasible with previously published strains of Gata3 reporter mice harboring disrupted alleles. The availability of hetero- and homozygous Gata3 reporter mice with an exceptionally bright fluorescent marker, allowed us to visualize allelic Gata3 expression in individual cells simply by flow cytometry. The unambiguous results obtained provide compelling evidence against previously postulated monoallelic Gata3 expression in early T lineage and hematopoietic stem cell subsets.
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Affiliation(s)
| | - Suresh Kumar
- Institute of Immunology, University Hospital, D-89081 Ulm, Germany; and
| | | | - Franziska Oliveri
- Institute of Immunology, University Hospital, D-89081 Ulm, Germany; and
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus Medical Center, NL-3000 CA Rotterdam, the Netherlands
| | - Franziska Beckel
- Institute of Immunology, University Hospital, D-89081 Ulm, Germany; and
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26
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Logical modeling of cell fate specification—Application to T cell commitment. Curr Top Dev Biol 2020; 139:205-238. [DOI: 10.1016/bs.ctdb.2020.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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27
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Thymic precursor cells generate acute myeloid leukemia in NUP98-PHF23/NUP98-HOXD13 double transgenic mice. Sci Rep 2019; 9:17213. [PMID: 31748606 PMCID: PMC6868234 DOI: 10.1038/s41598-019-53610-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/02/2019] [Indexed: 11/23/2022] Open
Abstract
Transgenic mice that express either a NUP98–PHF23 (NP23) or NUP98-HOXD13 (NHD13) fusion in the hematopoietic compartment develop a wide spectrum of leukemias, including myeloid, erythroid, megakaryocytic and lymphoid, at age 9–14 months. NP23-NHD13 double transgenic mice were generated by interbreeding NP23 and NHD13 mice. Remarkably, 100% of the NP23-NHD13 double transgenic mice developed acute myeloid leukemia (AML) within three months, characterized by replacement of the thymus with leukemic myeloblasts. The marked infiltration of thymus led to the intriguing hypothesis that AML generated in NP23-NHD13 mice arose in the thymus, as opposed to the bone marrow (BM). Transplantation of CD4-CD8- double negative (DN) thymocytes (which were also negative for Mac1 and Gr1) from leukemic NHD13/NP23 mice demonstrated that DN thymocytes could transmit AML, and limiting dilution studies showed that leukemia initiating cells were increased 14-fold in the thymus compared to BM. Further thymocyte fractionation demonstrated that DN1 and DN2, but not DN3 or DN4 fractions transmitted AML, and a marked expansion (100-fold) of Lineage-Sca1 + Kit + (LSK) cells in the thymus of the NP23-NHD13 mice. Taken together, these results show that the thymus of NP23-NHD13 mice acts as a reservoir for AML initiating cells and that thymic progenitors can transmit AML.
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28
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Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors. Cell Res 2019; 30:21-33. [PMID: 31729468 PMCID: PMC6951346 DOI: 10.1038/s41422-019-0251-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Achievement of immunocompetent and therapeutic T lymphopoiesis from pluripotent stem cells (PSCs) is a central aim in T cell regenerative medicine. To date, preferentially reconstituting T lymphopoiesis in vivo from PSCs remains a practical challenge. Here we documented that synergistic and transient expression of Runx1 and Hoxa9 restricted in the time window of endothelial-to-hematopoietic transition and hematopoietic maturation stages in a PSC differentiation scheme (iR9-PSC) in vitro induced preferential generation of engraftable hematopoietic progenitors capable of homing to thymus and developing into mature T cells in primary and secondary immunodeficient recipients. Single-cell transcriptome and functional analyses illustrated the cellular trajectory of T lineage induction from PSCs, unveiling the T-lineage specification determined at as early as hemogenic endothelial cell stage and identifying the bona fide pre-thymic progenitors. The induced T cells distributed normally in central and peripheral lymphoid organs and exhibited abundant TCRαβ repertoire. The regenerative T lymphopoiesis restored immune surveillance in immunodeficient mice. Furthermore, gene-edited iR9-PSCs produced tumor-specific T cells in vivo that effectively eradicated tumor cells. This study provides insight into universal generation of functional and therapeutic T cells from the unlimited and editable PSC source.
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29
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Abstract
Specification of multipotent blood precursor cells in postnatal mice to become committed T-cell precursors involves a gene regulatory network of several interacting but functionally distinct modules. Many links of this network have been defined by perturbation tests and by functional genomics. However, using the network model to predict real-life kinetics of the commitment process is still difficult, partly due to the tenacity of repressive chromatin states, and to the ability of transcription factors to affect each other's binding site choices through competitive recruitment to alternative sites ("coregulator theft"). To predict kinetics, future models will need to incorporate mechanistic information about chromatin state change dynamics and more sophisticated understanding of the proteomics and cooperative DNA site choices of transcription factor complexes.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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30
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Abstract
In this review, Rothenburg discusses the gene regulatory network and chromatin-based kinetic constraints that determine activities of transcription factors in the primary establishment of T-cell identity. T-cell development in mammals is a model for lineage choice and differentiation from multipotent stem cells. Although T-cell fate choice is promoted by signaling in the thymus through one dominant pathway, the Notch pathway, it entails a complex set of gene regulatory network and chromatin state changes even before the cells begin to express their signature feature, the clonal-specific T-cell receptors (TCRs) for antigen. This review distinguishes three developmental modules for T-cell development, which correspond to cell type specification, TCR expression and selection, and the assignment of cells to different effector types. The first is based on transcriptional regulatory network events, the second is dominated by somatic gene rearrangement and mutation and cell selection, and the third corresponds to establishing a poised state of latent regulator priming through an unknown mechanism. Interestingly, in different lineages, the third module can be deployed at variable times relative to the completion of the first two modules. This review focuses on the gene regulatory network and chromatin-based kinetic constraints that determine activities of transcription factors TCF1, GATA3, PU.1, Bcl11b, Runx1, and E proteins in the primary establishment of T-cell identity.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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31
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Zhou W, Yui MA, Williams BA, Yun J, Wold BJ, Cai L, Rothenberg EV. Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development. Cell Syst 2019; 9:321-337.e9. [PMID: 31629685 PMCID: PMC6932747 DOI: 10.1016/j.cels.2019.09.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/10/2019] [Accepted: 09/18/2019] [Indexed: 02/04/2023]
Abstract
Intrathymic T cell development converts multipotent precursors to committed pro-T cells, silencing progenitor genes while inducing T cell genes, but the underlying steps have remained obscure. Single-cell profiling was used to define the order of regulatory changes, employing single-cell RNA sequencing (scRNA-seq) for full-transcriptome analysis, plus sequential multiplexed single-molecule fluorescent in situ hybridization (seqFISH) to quantitate functionally important transcripts in intrathymic precursors. Single-cell cloning verified high T cell precursor frequency among the immunophenotypically defined "early T cell precursor" (ETP) population; a discrete committed granulocyte precursor subset was also distinguished. We established regulatory phenotypes of sequential ETP subsets, confirmed initial co-expression of progenitor with T cell specification genes, defined stage-specific relationships between cell cycle and differentiation, and generated a pseudotime model from ETP to T lineage commitment, supported by RNA velocity and transcription factor perturbations. This model was validated by developmental kinetics of ETP subsets at population and clonal levels. The results imply that multilineage priming is integral to T cell specification.
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Affiliation(s)
- Wen Zhou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mary A Yui
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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32
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Zhang L, Zhou F, Yu X, Zhu Y, Zhou Y, Liu J, Liu Y, Ma Q, Zhang Y, Wang W, Chen N. C/EBPα deficiency in podocytes aggravates podocyte senescence and kidney injury in aging mice. Cell Death Dis 2019; 10:684. [PMID: 31527620 PMCID: PMC6746733 DOI: 10.1038/s41419-019-1933-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/14/2019] [Accepted: 08/26/2019] [Indexed: 11/29/2022]
Abstract
Kidney aging leads to an increased incidence of end-stage renal disease (ESRD) in the elderly, and aging is a complex biological process controlled by signaling pathways and transcription factors. Podocyte senescence plays a central role in injury resulting from kidney aging. Here, we demonstrated the critical role of C/EBPα in podocyte senescence and kidney aging by generating a genetically modified mouse model of chronological aging in which C/EBPα was selectively deleted in podocytes and by overexpressing C/EBPα in cultured podocytes, in which premature senescence was induced by treatment with adriamycin. Moreover, we illuminated the mechanisms by which podocyte senescence causes tubular impairment by stimulating HK-2 cells with bovine serum albumin (BSA) and chloroquine. Our findings suggest that C/EBPα knockout in podocytes aggravates podocyte senescence through the AMPK/mTOR pathway, leading to glomerulosclerosis, and that subsequent albuminuria exacerbates the epithelial-mesenchymal transdifferentiation of senescent tubular cells by suppressing autophagy. These observations highlight the importance of C/EBPα as a new potential target in kidney aging.
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Affiliation(s)
- Liwen Zhang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
- Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
| | - Fangfang Zhou
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
- Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
| | - Xialian Yu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
- Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
| | - Yufei Zhu
- The Key Laboratory of Stem Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P.R. China
| | - Ying Zhou
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
- Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
| | - Jian Liu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
- Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
| | - Yunzi Liu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
- Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
| | - Qingyang Ma
- The Key Laboratory of Stem Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P.R. China
| | - Yuchao Zhang
- The Key Laboratory of Stem Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P.R. China
| | - Weiming Wang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China.
- Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China.
| | - Nan Chen
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
- Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, P.R. China
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33
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Peterson TV, Jaiswal MK, Beaman KD, Reynolds JM. Conditional Deletion of the V-ATPase a2-Subunit Disrupts Intrathymic T Cell Development. Front Immunol 2019; 10:1911. [PMID: 31456807 PMCID: PMC6700305 DOI: 10.3389/fimmu.2019.01911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/29/2019] [Indexed: 11/13/2022] Open
Abstract
Proper orchestration of T lymphocyte development is critical, as T cells underlie nearly all responses of the adaptive immune system. Developing thymocytes differentiate in response to environmental cues carried from cell surface receptors to the nucleus, shaping a distinct transcriptional program that defines their developmental outcome. Our recent work has identified a previously undescribed role for the vacuolar ATPase (V-ATPase) in facilitating the development of murine thymocytes progressing toward the CD4+ and CD8+ αβ T cell lineages. Vav1Cre recombinase-mediated deletion of the a2 isoform of the V-ATPase (a2V) in mouse hematopoietic cells leads to a specific and profound loss of peripheral CD4+ and CD8+ αβ T cells. Utilizing T cell-restricted LckCre and CD4Cre strains, we further traced this deficiency to the thymus and found that a2V plays a cell-intrinsic role throughout intrathymic development. Loss of a2V manifests as a partial obstruction in the double negative stage of T cell development, and later, a near complete failure of positive selection. These data deepen our understanding of the biological mechanisms that orchestrate T cell development and lend credence to the recent focus on V-ATPase as a potential chemotherapeutic target to combat proliferative potential in T cell lymphoblastic leukemias and autoimmune disease.
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Affiliation(s)
- Theodore V Peterson
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Mukesh K Jaiswal
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Kenneth D Beaman
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Joseph M Reynolds
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States.,Edward Hines, Jr. VA Hospital, Hines, IL, United States
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34
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Fernandez Garcia M, Moore CD, Schulz KN, Alberto O, Donague G, Harrison MM, Zhu H, Zaret KS. Structural Features of Transcription Factors Associating with Nucleosome Binding. Mol Cell 2019; 75:921-932.e6. [PMID: 31303471 DOI: 10.1016/j.molcel.2019.06.009] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/01/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Fate-changing transcription factors (TFs) scan chromatin to initiate new genetic programs during cell differentiation and reprogramming. Yet the protein structure domains that allow TFs to target nucleosomal DNA remain unexplored. We screened diverse TFs for binding to nucleosomes containing motif-enriched sequences targeted by pioneer factors in vivo. FOXA1, OCT4, ASCL1/E12α, PU1, CEBPα, and ZELDA display a range of nucleosome binding affinities that correlate with their cell reprogramming potential. We further screened 593 full-length human TFs on protein microarrays against different nucleosome sequences, followed by confirmation in solution, to distinguish among factors that bound nucleosomes, such as the neuronal AP-2α/β/γ, versus factors that only bound free DNA. Structural comparisons of DNA binding domains revealed that efficient nucleosome binders use short anchoring α helices to bind DNA, whereas weak nucleosome binders use unstructured regions and/or β sheets. Thus, specific modes of DNA interaction allow nucleosome scanning that confers pioneer activity to transcription factors.
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Affiliation(s)
- Meilin Fernandez Garcia
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Cedric D Moore
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katharine N Schulz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Oscar Alberto
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Greg Donague
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA.
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35
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Rothenberg EV. Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges. J Comput Biol 2019; 26:703-718. [PMID: 31063008 DOI: 10.1089/cmb.2019.0098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory network modeling has played a major role in advancing the understanding of developmental systems, by crystallizing structures of relevant extant information, by formally posing hypothetical functional relationships between network elements, and by offering clear predictive tests to improve understanding of the mechanisms driving developmental progression. Both ordinary differential equation (ODE)-based and Boolean models have also been highly successful in explaining dynamics within subcircuits of more complex processes. In a very small number of cases, gene regulatory network models of much more global scope have been proposed that successfully predict the dynamics of the processes establishing most of an embryonic body plan. Can such successes be expanded to very different developmental systems, including post-embryonic mammalian systems? This perspective discusses several problems that must be solved in more quantitative and predictive theoretical terms, to make this possible. These problems include: the effects of cellular history on chromatin state and how these affect gene accessibility; the dose dependence of activities of many transcription factors (a problem for Boolean models); stochasticity of some transcriptional outputs (a problem for simple ODE models); response timing delays due to epigenetic remodeling requirements; functionally different kinds of repression; and the regulatory syntax that governs responses of genes with multiple enhancers.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
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36
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Rodríguez-Caparrós A, García V, Casal Á, López-Ros J, García-Mariscal A, Tani-ichi S, Ikuta K, Hernández-Munain C. Notch Signaling Controls Transcription via the Recruitment of RUNX1 and MYB to Enhancers during T Cell Development. THE JOURNAL OF IMMUNOLOGY 2019; 202:2460-2472. [DOI: 10.4049/jimmunol.1801650] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/11/2019] [Indexed: 12/11/2022]
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37
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Ye Y, Kang X, Bailey J, Li C, Hong T. An enriched network motif family regulates multistep cell fate transitions with restricted reversibility. PLoS Comput Biol 2019; 15:e1006855. [PMID: 30845219 PMCID: PMC6424469 DOI: 10.1371/journal.pcbi.1006855] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/19/2019] [Accepted: 02/07/2019] [Indexed: 12/16/2022] Open
Abstract
Multistep cell fate transitions with stepwise changes of transcriptional profiles are common to many developmental, regenerative and pathological processes. The multiple intermediate cell lineage states can serve as differentiation checkpoints or branching points for channeling cells to more than one lineages. However, mechanisms underlying these transitions remain elusive. Here, we explored gene regulatory circuits that can generate multiple intermediate cellular states with stepwise modulations of transcription factors. With unbiased searching in the network topology space, we found a motif family containing a large set of networks can give rise to four attractors with the stepwise regulations of transcription factors, which limit the reversibility of three consecutive steps of the lineage transition. We found that there is an enrichment of these motifs in a transcriptional network controlling the early T cell development, and a mathematical model based on this network recapitulates multistep transitions in the early T cell lineage commitment. By calculating the energy landscape and minimum action paths for the T cell model, we quantified the stochastic dynamics of the critical factors in response to the differentiation signal with fluctuations. These results are in good agreement with experimental observations and they suggest the stable characteristics of the intermediate states in the T cell differentiation. These dynamical features may help to direct the cells to correct lineages during development. Our findings provide general design principles for multistep cell linage transitions and new insights into the early T cell development. The network motifs containing a large family of topologies can be useful for analyzing diverse biological systems with multistep transitions. The functions of cells are dynamically controlled in many biological processes including development, regeneration and disease progression. Cell fate transition, or the switch of cellular functions, often involves multiple steps. The intermediate stages of the transition provide the biological systems with the opportunities to regulate the transitions in a precise manner. These transitions are controlled by key regulatory genes of which the expression shows stepwise patterns, but how the interactions of these genes can determine the multistep processes was unclear. Here, we present a comprehensive analysis on the design principles of gene circuits that govern multistep cell fate transition. We found a large network family with common structural features that can generate systems with the ability to control three consecutive steps of the transition. We found that this type of networks is enriched in a gene circuit controlling the development of T lymphocyte, a crucial type of immune cells. We performed mathematical modeling using this gene circuit and we recapitulated the stepwise and irreversible loss of stem cell properties of the developing T lymphocytes. Our findings can be useful to analyze a wide range of gene regulatory networks controlling multistep cell fate transitions.
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Affiliation(s)
- Yujie Ye
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Xin Kang
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China.,School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Jordan Bailey
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chunhe Li
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China.,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America.,National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee, United States of America
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38
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Rothenberg EV, Hosokawa H, Ungerbäck J. Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development. Front Immunol 2019; 10:228. [PMID: 30842770 PMCID: PMC6391351 DOI: 10.3389/fimmu.2019.00228] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
PU.1 is an ETS-family transcription factor that plays a broad range of roles in hematopoiesis. A direct regulator of myeloid, dendritic-cell, and B cell functional programs, and a well-known antagonist of terminal erythroid cell differentiation, it is also expressed in the earliest stages of T-cell development of each cohort of intrathymic pro-T cells. Its expression in this context appears to give T-cell precursors initial, transient access to myeloid and dendritic cell developmental competence and therefore to represent a source of antagonism or delay of T-cell lineage commitment. However, it has remained uncertain until recently why T-cell development is also intensely dependent upon PU.1. Here, we review recent work that sheds light on the molecular biology of PU.1 action across the genome in pro-T cells and identifies the genes that depend on PU.1 for their correct regulation. This work indicates modes of chromatin engagement, pioneering, and cofactor recruitment (“coregulator theft”) by PU.1 as well as gene network interactions that not only affect specific target genes but also have system-wide regulatory consequences, amplifying the impact of PU.1 beyond its own direct binding targets. The genes directly regulated by PU.1 also suggest a far-reaching transformation of cell biology and signaling potential between the early stages of T-cell development when PU.1 is expressed and when it is silenced. These cell-biological functions can be important to distinguish fetal from adult T-cell development and have the potential to illuminate aspects of thymic function that have so far remained the most mysterious.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Jonas Ungerbäck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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Hosokawa H, Ungerbäck J, Wang X, Matsumoto M, Nakayama KI, Cohen SM, Tanaka T, Rothenberg EV. Transcription Factor PU.1 Represses and Activates Gene Expression in Early T Cells by Redirecting Partner Transcription Factor Binding. Immunity 2019; 48:1119-1134.e7. [PMID: 29924977 DOI: 10.1016/j.immuni.2018.04.024] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/21/2018] [Accepted: 04/19/2018] [Indexed: 01/09/2023]
Abstract
Transcription factors normally regulate gene expression through their action at sites where they bind to DNA. However, the balance of activating and repressive functions that a transcription factor can mediate is not completely understood. Here, we showed that the transcription factor PU.1 regulated gene expression in early T cell development both by recruiting partner transcription factors to its own binding sites and by depleting them from the binding sites that they preferred when PU.1 was absent. The removal of partner factors Satb1 and Runx1 occurred primarily from sites where PU.1 itself did not bind. Genes linked to sites of partner factor "theft" were enriched for genes that PU.1 represses despite lack of binding, both in a model cell line system and in normal T cell development. Thus, system-level competitive recruitment dynamics permit PU.1 to affect gene expression both through its own target sites and through action at a distance.
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Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonas Ungerbäck
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Division of Molecular Hematology, Lund University, Sweden
| | - Xun Wang
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Japan
| | - Sarah M Cohen
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Japan; AMED-CREST, AMED, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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40
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Kallies A, Nutt SL. Transcription Factor Theft-PU.1 Caught Red-Handed. Immunity 2019; 48:1063-1065. [PMID: 29924967 DOI: 10.1016/j.immuni.2018.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The mechanistic understanding of gene-expression regulation is still evolving. In this issue of Immunity, Hosokawa et al. (2018) reveal that PU.1 represses transcription indirectly during early T cell development by "stealing" other regulators such as Runx1 and Satb1 from their DNA binding sites.
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Affiliation(s)
- Axel Kallies
- Department of Microbiology and Immunology, The University of Melbourne and The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, Melbourne VIC, Australia.
| | - Stephen L Nutt
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, Melbourne VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
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41
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Hosokawa H, Romero-Wolf M, Yui MA, Ungerbäck J, Quiloan MLG, Matsumoto M, Nakayama KI, Tanaka T, Rothenberg EV. Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16. Nat Immunol 2018; 19:1427-1440. [PMID: 30374131 PMCID: PMC6240390 DOI: 10.1038/s41590-018-0238-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Abstract
Multipotent progenitors confirm their T cell-lineage identity in the DN2 pro-T cell stages, when expression of the essential transcription factor Bcl11b begins. In vivo and in vitro stage-specific deletions globally identified Bcl11b-controlled target genes in pro-T cells. Proteomic analysis revealed that Bcl11b associates with multiple cofactors, and that its direct action was needed to recruit these cofactors to selective target sites. These sites of Bcl11b-dependent cofactor recruitment were enriched near functionally regulated target genes, and deletion of individual cofactors relieved repression of many Bcl11b-repressed genes. Runx1 collaborated with Bcl11b most frequently for both activation and repression. In parallel, Bcl11b indirectly regulated a subset of target genes by a gene network circuit via Id2 and Zbtb16 (encoding PLZF), which were directly repressed by Bcl11b and controlled distinct alternative programs. Thus, this study defines the molecular basis of direct and indirect Bcl11b actions that promote T cell identity and block alternative potentials.
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Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Maile Romero-Wolf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mary A Yui
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonas Ungerbäck
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Maria L G Quiloan
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Chiba University, Chuo-ku, Chiba, Japan.,AMED-CREST, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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42
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Ungerbäck J, Hosokawa H, Wang X, Strid T, Williams BA, Sigvardsson M, Rothenberg EV. Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by SPI1 (PU.1). Genome Res 2018; 28:1508-1519. [PMID: 30171019 PMCID: PMC6169891 DOI: 10.1101/gr.231423.117] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 08/30/2018] [Indexed: 01/09/2023]
Abstract
SPI1 (also known as PU.1) is a dominant but transient regulator in early T-cell precursors and a potent transcriptional controller of developmentally important pro-T-cell genes. Before T-lineage commitment, open chromatin is frequently occupied by PU.1, and many PU.1 sites lose accessibility when PU.1 is later down-regulated. Pioneering activity of PU.1 was tested in this developmentally dynamic context by quantitating the relationships between PU.1 occupancy and site quality and accessibility as PU.1 levels naturally declined in pro-T-cell development and by using stage-specific gain- and loss-of-function perturbations to relate binding to effects on target genes. PU.1 could bind closed genomic sites, but rapidly opened many of them, despite the absence of its frequent collaborator, CEBPA. RUNX motifs and RUNX1 binding were often linked to PU.1 at open sites, but highly expressed PU.1 could bind its sites without RUNX1. The dynamic properties of PU.1 engagements implied that PU.1 binding affinity and concentration determine its occupancy choices, but with quantitative trade-offs for occupancy between site sequence quality and stage-dependent site accessibility in chromatin. At nonpromoter sites, PU.1 binding criteria were more stringent than at promoters, and PU.1 was also much more effective as a transcriptional regulator at nonpromoter sites where local chromatin accessibility depended on the presence of PU.1. Notably, closed chromatin presented a qualitative barrier to occupancy by the PU.1 DNA-binding domain alone. Thus, effective pioneering at closed chromatin sites also depends on requirements beyond site recognition, served by non-DNA-binding domains of PU.1.
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Affiliation(s)
- Jonas Ungerbäck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA.,Division of Molecular Hematology, Lund University, SE-221 84 Lund, Sweden
| | - Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Xun Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Tobias Strid
- Division of Molecular Hematology, Lund University, SE-221 84 Lund, Sweden
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund University, SE-221 84 Lund, Sweden.,Department of Clinical and Experimental Medicine, Linköping University, SE-581 83 Linköping, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Stage-specific roles for Zmiz1 in Notch-dependent steps of early T-cell development. Blood 2018; 132:1279-1292. [PMID: 30076146 DOI: 10.1182/blood-2018-02-835850] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/29/2018] [Indexed: 12/15/2022] Open
Abstract
Notch1 signaling must elevate to high levels in order to drive the proliferation of CD4-CD8- double-negative (DN) thymocytes and progression to the CD4+CD8+ double-positive (DP) stage through β-selection. During this critical phase of pre-T-cell development, which is also known as the DN-DP transition, it is unclear whether the Notch1 transcriptional complex strengthens its signal output as a discrete unit or through cofactors. We previously showed that the protein inhibitor of activated STAT-like coactivator Zmiz1 is a context-dependent cofactor of Notch1 in T-cell leukemia. We also showed that withdrawal of Zmiz1 generated an early T-lineage progenitor (ETP) defect. Here, we show that this early defect seems inconsistent with loss-of-Notch1 function. In contrast, at the later pre-T-cell stage, withdrawal of Zmiz1 impaired the DN-DP transition by inhibiting proliferation, like withdrawal of Notch. In pre-T cells, but not ETPs, Zmiz1 cooperatively regulated Notch1 target genes Hes1, Lef1, and Myc. Enforced expression of either activated Notch1 or Myc partially rescued the Zmiz1-deficient DN-DP defect. We identified residues in the tetratricopeptide repeat (TPR) domain of Zmiz1 that bind Notch1. Mutating only a single residue impaired the Zmiz1-Notch1 interaction, Myc induction, the DN-DP transition, and leukemic proliferation. Similar effects were seen using a dominant-negative TPR protein. Our studies identify stage-specific roles of Zmiz1. Zmiz1 is a context-specific cofactor for Notch1 during Notch/Myc-dependent thymocyte proliferation, whether normal or malignant. Finally, we highlight a vulnerability in leukemic cells that originated from a developmentally important Zmiz1-Notch1 interaction that is hijacked during transformation from normal pre-T cells.
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44
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Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. Proc Natl Acad Sci U S A 2018; 114:5800-5807. [PMID: 28584128 DOI: 10.1073/pnas.1610617114] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
T-cell development from hematopoietic progenitors depends on multiple transcription factors, mobilized and modulated by intrathymic Notch signaling. Key aspects of T-cell specification network architecture have been illuminated through recent reports defining roles of transcription factors PU.1, GATA-3, and E2A, their interactions with Notch signaling, and roles of Runx1, TCF-1, and Hes1, providing bases for a comprehensively updated model of the T-cell specification gene regulatory network presented herein. However, the role of lineage commitment factor Bcl11b has been unclear. We use self-organizing maps on 63 RNA-seq datasets from normal and perturbed T-cell development to identify functional targets of Bcl11b during commitment and relate them to other regulomes. We show that both activation and repression target genes can be bound by Bcl11b in vivo, and that Bcl11b effects overlap with E2A-dependent effects. The newly clarified role of Bcl11b distinguishes discrete components of commitment, resolving how innate lymphoid, myeloid, and dendritic, and B-cell fate alternatives are excluded by different mechanisms.
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Hosokawa H, Rothenberg EV. Cytokines, Transcription Factors, and the Initiation of T-Cell Development. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028621. [PMID: 28716889 DOI: 10.1101/cshperspect.a028621] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multipotent blood progenitor cells migrate into the thymus and initiate the T-cell differentiation program. T-cell progenitor cells gradually acquire T-cell characteristics while shedding their multipotentiality for alternative fates. This process is supported by extracellular signaling molecules, including Notch ligands and cytokines, provided by the thymic microenvironment. T-cell development is associated with dynamic change of gene regulatory networks of transcription factors, which interact with these environmental signals. Together with Notch or pre-T-cell-receptor (TCR) signaling, cytokines always control proliferation, survival, and differentiation of early T cells, but little is known regarding their cross talk with transcription factors. However, recent results suggest ways that cytokines expressed in distinct intrathymic niches can specifically modulate key transcription factors. This review discusses how stage-specific roles of cytokines and transcription factors can jointly guide development of early T cells.
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Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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Abstract
PURPOSE OF REVIEW Hematopoietic stem cells (HSCs) possess two fundamental characteristics, the capacity for self-renewal and the sustained production of all blood cell lineages. The fine balance between HSC expansion and lineage specification is dynamically regulated by the interplay between external and internal stimuli. This review introduces recent advances in the roles played by the stem cell niche, regulatory transcriptional networks, and metabolic pathways in governing HSC self-renewal, commitment, and lineage differentiation. We will further focus on discoveries made by studying hematopoiesis at single-cell resolution. RECENT FINDINGS HSCs require the support of an interactive milieu with their physical position within the perivascular niche dynamically regulating HSC behavior. In these microenvironments, transcription factor networks and nutrient-mediated regulation of energy resources, signaling pathways, and epigenetic status govern HSC quiescence and differentiation. Once HSCs begin their lineage specification, single-cell analyses show that they do not become oligopotent but rather, differentiate directly into committed unipotent progenitors. SUMMARY The diversity of transcriptional networks and metabolic pathways in HSCs and their downstream progeny allows a high level of plasticity in blood differentiation. The intricate interactions between these pathways, within the perivascular niche, broaden the specification of HSCs in pathological and stressed conditions.
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Rothenberg EV. Fitting structure to function in gene regulatory networks. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2017; 39:37. [PMID: 29038942 PMCID: PMC5660880 DOI: 10.1007/s40656-017-0164-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cascades of transcriptional regulation are the common source of the forward drive in all developmental systems. Increases in complexity and specificity of gene expression at successive stages are based on the collaboration of varied combinations of transcription factors already expressed in the cells to turn on new genes, and the logical relationships between the transcription factors acting and becoming newly expressed from stage to stage are best visualized as gene regulatory networks. However, gene regulatory networks used in different developmental contexts underlie processes that actually operate through different sets of rules, which affect the kinetics, synchronicity, and logical properties of individual network nodes. Contrasting early embryonic development in flies and sea urchins with adult mammalian hematopoietic development from stem cells, major differences are seen in transcription factor dosage dependence, the silencing or damping impacts of repression, and the impact of cellular regulatory history on the parts of the genome that are accessible to transcription factor action in a given cell type. These different features not only affect the kinds of models that can illuminate developmental mechanisms in the respective biological systems, but also reflect the evolutionary needs of these biological systems to optimize different aspects of development.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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48
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Berthault C, Ramond C, Burlen-Defranoux O, Soubigou G, Chea S, Golub R, Pereira P, Vieira P, Cumano A. Asynchronous lineage priming determines commitment to T cell and B cell lineages in fetal liver. Nat Immunol 2017; 18:1139-1149. [PMID: 28825702 DOI: 10.1038/ni.3820] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/31/2017] [Indexed: 12/15/2022]
Abstract
The molecular events that initiate lymphoid-lineage specification remain unidentified because the stages of differentiation during which lineage commitment occurs are difficult to characterize. We isolated fetal liver progenitor cells undergoing restriction of their differentiation potential toward the T cell-innate lymphoid cell lineage or the B cell lineage. Transcripts that defined the molecular signatures of these two subsets were sequentially upregulated in lympho-myeloid precursor cells and in common lymphoid progenitor cells, respectively, and this preceded lineage restriction; this indicates that T cell-versus-B cell commitment is not a binary fate 'decision'. The T cell-bias and B cell-bias transcriptional programs were frequently co-expressed in common lymphoid progenitor cells and were segregated in subsets biased toward T cell differentiation or B cell differentiation, after interleukin 7 (IL-7) signaling that controlled the number of progenitor cells engaging in T cell differentiation versus B cell differentiation.
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Affiliation(s)
- Claire Berthault
- Unit for Lymphopoiesis, Pasteur Institute, Paris, France. Immunology department.,INSERM U1223, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Cyrille Ramond
- Unit for Lymphopoiesis, Pasteur Institute, Paris, France. Immunology department.,INSERM U1223, Paris, France.,Université Pierre et Marie Curie, Paris, France
| | - Odile Burlen-Defranoux
- Unit for Lymphopoiesis, Pasteur Institute, Paris, France. Immunology department.,INSERM U1223, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Guillaume Soubigou
- Département Génomes et Génétique, Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
| | - Sylvestre Chea
- Unit for Lymphopoiesis, Pasteur Institute, Paris, France. Immunology department.,INSERM U1223, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Rachel Golub
- Unit for Lymphopoiesis, Pasteur Institute, Paris, France. Immunology department.,INSERM U1223, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Pablo Pereira
- Unit for Lymphopoiesis, Pasteur Institute, Paris, France. Immunology department.,INSERM U1223, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Paulo Vieira
- Unit for Lymphopoiesis, Pasteur Institute, Paris, France. Immunology department.,INSERM U1223, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Ana Cumano
- Unit for Lymphopoiesis, Pasteur Institute, Paris, France. Immunology department.,INSERM U1223, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
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Seki M, Kimura S, Isobe T, Yoshida K, Ueno H, Nakajima-Takagi Y, Wang C, Lin L, Kon A, Suzuki H, Shiozawa Y, Kataoka K, Fujii Y, Shiraishi Y, Chiba K, Tanaka H, Shimamura T, Masuda K, Kawamoto H, Ohki K, Kato M, Arakawa Y, Koh K, Hanada R, Moritake H, Akiyama M, Kobayashi R, Deguchi T, Hashii Y, Imamura T, Sato A, Kiyokawa N, Oka A, Hayashi Y, Takagi M, Manabe A, Ohara A, Horibe K, Sanada M, Iwama A, Mano H, Miyano S, Ogawa S, Takita J. Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia. Nat Genet 2017; 49:1274-1281. [PMID: 28671687 DOI: 10.1038/ng.3900] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/24/2017] [Indexed: 12/12/2022]
Abstract
The outcome of treatment-refractory and/or relapsed pediatric T cell acute lymphoblastic leukemia (T-ALL) is extremely poor, and the genetic basis for this is not well understood. Here we report comprehensive profiling of 121 cases of pediatric T-ALL using transcriptome and/or targeted capture sequencing, through which we identified new recurrent gene fusions involving SPI1 (STMN1-SPI1 and TCF7-SPI1). Cases positive for fusions involving SPI1 (encoding PU.1), accounting for 3.9% (7/181) of the examined pediatric T-ALL cases, showed a double-negative (DN; CD4-CD8-) or CD8+ single-positive (SP) phenotype and had uniformly poor overall survival. These cases represent a subset of pediatric T-ALL distinguishable from the known T-ALL subsets in terms of expression of genes involved in T cell precommitment, establishment of T cell identity, and post-β-selection maturation and with respect to mutational profile. PU.1 fusion proteins retained transcriptional activity and, when constitutively expressed in mouse stem/progenitor cells, induced cell proliferation and resulted in a maturation block. Our findings highlight a unique role of SPI1 fusions in high-risk pediatric T-ALL.
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Affiliation(s)
- Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroo Ueno
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yaeko Nakajima-Takagi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Changshan Wang
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Lin Lin
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ayana Kon
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Shiozawa
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyoko Masuda
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuki Arakawa
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Ryoji Hanada
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Hiroshi Moritake
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Masaharu Akiyama
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Ryoji Kobayashi
- Department of Pediatrics, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Takao Deguchi
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Yoshiko Hashii
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Atsushi Sato
- Department of Hematology and Oncology, Miyagi Children's Hospital, Sendai, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | | | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | - Akira Ohara
- Department of Pediatrics, Toho University, Tokyo, Japan
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masashi Sanada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Mano
- Department of Cellular Signaling, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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The Regulatory Capacity of Bivalent Genes-A Theoretical Approach. Int J Mol Sci 2017; 18:ijms18051069. [PMID: 28513551 PMCID: PMC5454979 DOI: 10.3390/ijms18051069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023] Open
Abstract
Bivalent genes are frequently associated with developmental and lineage specification processes. Resolving their bivalency enables fast changes in their expression, which potentially can trigger cell fate decisions. Here, we provide a theoretical model of bivalency that allows for predictions on the occurrence, stability and regulatory capacity of this prominent modification state. We suggest that bivalency enables balanced gene expression heterogeneity that constitutes a prerequisite of robust lineage priming in somatic stem cells. Moreover, we demonstrate that interactions between the histone and DNA methylation machineries together with the proliferation activity control the stability of the bivalent state and can turn it into an unmodified state. We suggest that deregulation of these interactions underlies cell transformation processes as associated with acute myeloid leukemia (AML) and provide a model of AML blast formation following deregulation of the Ten-eleven Translocation (TET) pathway.
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